Clockor2

Clockor2 conducts root-to-tip regression to assess the degree to which molecular sequence data behave in a clock-like fashion, enabling users to fit local and global strict molecular clocks.

Key Features:

• Root-to-tip regression: Performs RTT regression to evaluate clock-like behavior in molecular sequence data sampled at different points in time.
• Local and global molecular clock fitting: Fits both local and global strict molecular clocks to accommodate genomic datasets that sample beyond the assumption of homogeneous host populations.
• Scalable performance: Handles phylogenetic trees of up to the order of 10^4 tips with significant speed increases compared with other RTT regression applications.
• Client-side processing: All data processing occurs on the client-side, ensuring that data never leave the user's computer.

Scientific Applications:

• Molecular clock calibration: Uses sampling times from molecular sequence data of rapidly evolving organisms to calibrate molecular clocks.
• Clock-like behavior assessment: Evaluates whether molecular data exhibit clock-like evolution prior to downstream phylogenetic dating analyses.
• Genomic dataset analysis: Handles complex genomic datasets with heterogeneous sampling that violate assumptions of homogeneous host populations.

Methodology:

Clockor2 implements root-to-tip regression for inferring global and local strict molecular clocks. The method uses sampling times from molecular sequence data to calibrate clocks and assess temporal signal in phylogenetic trees.